There are 4 files here:
align: alignment file from assembling all the reads from RR, RS libraries (This file is too large for ANGEL site, I put it at ftp://ftp.tigr.org/private/YXIAO/Raphanus/)
type.SNPonly2: contigs contain any possible SNP
SNPonly_w_types: contigs contain at least one possible SNP types as defined below
SNPonly_w_type_all: contigs with possible SNPs are all defined types

SNP types:
all_RS_reads(one base)        all_RR_reads(another base)    TYPE1
all_RS1_reads(one base)       all_RS2_reads(another base)   TYPE2
all_RS1_reads(one base)       all_RS3_reads(another base)   TYPE3
all_RS2_reads(one base)       all_RS3_reads(another base)   TYPE4
all_RR1_reads(one base)       all_RR2_reads(another base)   TYPE5
all_RR1_reads(one base)       all_RR3_reads(another base)   TYPE6
all_RR1_reads(one base)       all_RR4_reads(another base)   TYPE7
all_RR2_reads(one base)       all_RR3_reads(another base)   TYPE8
all_RR2_reads(one base)       all_RR4_reads(another base)   TYPE9
all_RR3_reads(one base)       all_RR4_reads(another base)   TYPE10
snp within just RS1_reads    TYPE11
snp within just RS2_reads    TYPE12
snp within just RS3_reads    TYPE13
snp within just RR1_reads    TYPE14
snp within just RR2_reads    TYPE15
snp within just RR3_reads    TYPE16
snp within just RR4_reads    TYPE17

RS1: AR library
RS2: RS library
RS3: RT library
RR1: CS library
RR2: MS library
RR3: NY library
RR4: PB library
